5DMG

X-RAY STRUCTURE OF THE FAB FRAGMENT OF THE ANTI TAU ANTIBODY RB86 IN COMPLEX WITH THE PHOSPHORYLATED TAU PEPTIDE (416-430)

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E	PF07654	e5dmgE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
E	PF07686	e5dmgE2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
A [auth H]	PF07654	e5dmgH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
A [auth H]	PF07686	e5dmgH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C	PF07654	e5dmgC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
C	PF07686	e5dmgC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B [auth L]	PF07654	e5dmgL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B [auth L]	PF07686	e5dmgL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D	PF07654	e5dmgD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
D	PF07686	e5dmgD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
F	PF07654	e5dmgF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
F	PF07686	e5dmgF2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A [auth H], C, E	RB86 Fab	VH-CH1	Oryctolagus cuniculus (rabbit)	IGHV1S6901, IGHJ402, IGHG101, IGHG102, IGHG104, IGHG105	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)
B [auth L], D, F	RB86 Fab	L-KAPPA	Oryctolagus cuniculus (rabbit)	IGKV1S101, IGKJ1-202, IGKJ1-201, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H], C, E	Heavy Chain	IGHV1	-	microtubule-associated protein	SAbDab (2024-04-26)
B [auth L], D, F	Light Chain	IGKV1	Kappa	microtubule-associated protein	SAbDab (2024-04-26)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H], C, E	RB86 antibody Fab fragment heavy chain	-	-	-
B [auth L], D, F	RB86 antibody Fab fragment light chain	-	-	-
G [auth Z], H [auth P], I [auth X]	Microtubule-associated protein	cytoskeletal protein binding microtubule binding protein binding binding tubulin binding microtubule lateral binding sequence-specific DNA binding DNA binding organic cyclic compound binding nucleic acid binding protein-folding chaperone binding SH3 domain binding protein domain specific binding DNA secondary structure binding cytoskeletal protein binding microtubule binding protein binding binding tubulin binding microtubule lateral binding sequence-specific DNA binding DNA binding organic cyclic compound binding nucleic acid binding protein-folding chaperone binding SH3 domain binding protein domain specific binding DNA secondary structure binding minor groove of adenine-thymine-rich DNA binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding protein phosphatase binding phosphatase binding enzyme binding protein phosphatase 2A binding kinase binding protein kinase binding single-stranded DNA binding protein-macromolecule adaptor activity molecular adaptor activity dynactin binding identical protein binding Hsp90 protein binding heat shock protein binding apolipoprotein binding RNA binding lipoprotein particle binding protein-containing complex binding protein-lipid complex binding double-stranded DNA binding actin binding histone-dependent DNA binding	establishment of organelle localization cellular localization organelle transport along microtubule transport intracellular transport plus-end-directed organelle transport along microtubule establishment of localization localization organelle localization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport cellular process establishment of organelle localization cellular localization organelle transport along microtubule transport intracellular transport plus-end-directed organelle transport along microtubule establishment of localization localization organelle localization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport cellular process microtubule-based movement microtubule-based process regulation of biological process regulation of cellular process cellular metabolic process reactive oxygen species metabolic process biological regulation positive regulation of biological process regulation of superoxide metabolic process regulation of cellular metabolic process positive regulation of cellular metabolic process positive regulation of reactive oxygen species metabolic process superoxide metabolic process positive regulation of metabolic process superoxide anion generation metabolic process positive regulation of superoxide anion generation regulation of superoxide anion generation regulation of metabolic process regulation of reactive oxygen species metabolic process positive regulation of cellular process cellular component biogenesis cellular component organization cellular component assembly inclusion body assembly cellular component organization or biogenesis neurofibrillary tangle assembly cellular response to endogenous stimulus cellular response to growth factor stimulus response to stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus cellular response to brain-derived neurotrophic factor stimulus response to nerve growth factor response to growth factor cellular response to stimulus cellular response to heat cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus developmental process regulation of cellular component organization regulation of developmental process organelle fission mitochondrial fission regulation of organelle organization anatomical structure morphogenesis organelle organization regulation of mitochondrial fission regulation of mitochondrion organization anatomical structure development regulation of anatomical structure morphogenesis mitochondrion organization axon extension multicellular organismal process positive regulation of nervous system development regulation of growth axonogenesis regulation of cellular component size developmental growth cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of developmental process multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation positive regulation of cell projection organization regulation of biological quality positive regulation of developmental growth system development regulation of cell projection organization positive regulation of cell development nervous system development developmental growth involved in morphogenesis generation of neurons positive regulation of multicellular organismal process regulation of neuron projection development positive regulation of cellular component organization cellular developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis regulation of axon extension regulation of nervous system development neurogenesis regulation of extent of cell growth positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process positive regulation of axon extension positive regulation of axonogenesis regulation of cell size neuron projection extension regulation of multicellular organismal development regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth positive regulation of cell growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation positive regulation of growth neuron development regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size behavior system process learning or memory nervous system process cognition memory astrocyte differentiation astrocyte activation glial cell development astrocyte development gliogenesis defense response cell activation central nervous system development glial cell differentiation glial cell activation inflammatory response neuroinflammatory response myeloid leukocyte activation leukocyte activation macrophage activation immune system process leukocyte activation involved in inflammatory response microglial cell activation establishment of mitochondrion localization axonal transport mitochondrion localization establishment of mitochondrion localization, microtubule-mediated axo-dendritic transport mitochondrion transport along microtubule axonal transport of mitochondrion protein polymerization protein-containing complex organization protein-containing complex assembly regulation of catalytic activity positive regulation of protein metabolic process positive regulation of peptidase activity positive regulation of cysteine-type endopeptidase activity involved in apoptotic process regulation of primary metabolic process positive regulation of molecular function regulation of cysteine-type endopeptidase activity involved in apoptotic process organic substance metabolic process regulation of proteolysis proteolysis regulation of endopeptidase activity positive regulation of macromolecule metabolic process protein metabolic process activation of cysteine-type endopeptidase activity involved in apoptotic process regulation of cysteine-type endopeptidase activity organonitrogen compound metabolic process regulation of protein metabolic process regulation of peptidase activity positive regulation of catalytic activity primary metabolic process regulation of macromolecule metabolic process regulation of molecular function positive regulation of hydrolase activity positive regulation of cysteine-type endopeptidase activity regulation of hydrolase activity positive regulation of endopeptidase activity positive regulation of proteolysis macromolecule metabolic process amyloid fibril formation supramolecular fiber organization cell junction organization synapse organization negative regulation of biological process negative regulation of phosphate metabolic process negative regulation of catalytic activity regulation of transferase activity negative regulation of cellular metabolic process negative regulation of kinase activity negative regulation of transferase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of cellular process phosphorus metabolic process phosphorylation negative regulation of metabolic process negative regulation of molecular function regulation of kinase activity negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process negative regulation of phosphorylation microtubule cytoskeleton organization cytoplasmic microtubule organization cytoskeleton organization response to metal ion response to chemical response to lead ion response to inorganic substance regulation of signaling signaling regulation of signal transduction intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus calcium-mediated signaling intracellular signaling cassette regulation of calcium-mediated signaling regulation of cell communication signal transduction modulation of chemical synaptic transmission negative regulation of signaling negative regulation of synaptic transmission negative regulation of cell communication synaptic signaling regulation of synaptic plasticity trans-synaptic signaling cell-cell signaling chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling long-term synaptic depression regulation of long-term synaptic depression cellular biosynthetic process organic substance biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process positive regulation of phosphorylation regulation of lipid metabolic process positive regulation of phosphate metabolic process regulation of lipid kinase activity positive regulation of lipid metabolic process positive regulation of lipid kinase activity positive regulation of transferase activity positive regulation of phosphorus metabolic process regulation of diacylglycerol kinase activity positive regulation of kinase activity positive regulation of diacylglycerol kinase activity lipid metabolic process protein complex oligomerization protein homooligomerization nucleobase-containing compound metabolic process organic cyclic compound metabolic process ncRNA metabolic process RNA metabolic process rRNA metabolic process nucleic acid metabolic process DNA damage response negative regulation of cellular component organization negative regulation of developmental process negative regulation of organelle organization negative regulation of mitochondrial fission central nervous system neuron development central nervous system neuron differentiation negative regulation of membrane potential regulation of mitochondrial membrane potential negative regulation of mitochondrial membrane potential regulation of membrane potential microtubule polymerization microtubule polymerization or depolymerization positive regulation of organelle organization regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly positive regulation of protein polymerization positive regulation of microtubule polymerization or depolymerization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of microtubule-based process positive regulation of supramolecular fiber organization regulation of cellular component biogenesis positive regulation of microtubule polymerization regulation of protein polymerization regulation of microtubule polymerization regulation of supramolecular fiber organization regulation of microtubule cytoskeleton organization stress granule assembly organelle assembly non-membrane-bounded organelle assembly protein localization negative regulation of establishment of protein localization to mitochondrion regulation of localization establishment of protein localization regulation of protein localization cellular macromolecule localization negative regulation of protein localization regulation of establishment of protein localization negative regulation of establishment of protein localization regulation of establishment of protein localization to mitochondrion establishment of protein localization to organelle regulation of cellular localization macromolecule localization protein localization to organelle protein localization to mitochondrion establishment of protein localization to mitochondrion protein acylation protein acetylation macromolecule modification protein modification process internal protein amino acid acetylation cell junction assembly synapse assembly regulation of cellular response to heat regulation of cellular response to stress regulation of response to stress regulation of protein modification process macromolecule deacylation protein deacetylation negative regulation of tubulin deacetylation regulation of protein deacetylation tubulin deacetylation negative regulation of protein modification process negative regulation of protein metabolic process regulation of tubulin deacetylation protein deacylation mitochondrion distribution intracellular distribution of mitochondria protein localization to synapse positive regulation of protein localization to synapse regulation of protein localization to synapse positive regulation of protein localization protein localization to cell junction chromosome organization regulation of chromosome organization cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound response to reactive oxygen species cellular response to reactive oxygen species response to oxidative stress cellular response to chemical stimulus catabolic process autophagy regulation of catabolic process regulation of autophagy cellular catabolic process regulation of cellular catabolic process process utilizing autophagic mechanism	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex cytoskeleton tubulin complex intracellular non-membrane-bounded organelle non-membrane-bounded organelle cytoplasm cytosol neuron spine synapse neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection postsynapse cell junction dendrite dendritic tree cell body neuron projection cytoplasm axon axon cytoplasm cytoplasmic region plasma membrane bounded cell projection cytoplasm cell periphery plasma membrane membrane nuclear periphery membrane microdomain membrane raft main axon cytoplasmic ribonucleoprotein granule supramolecular complex ribonucleoprotein granule extracellular region neurofibrillary tangle inclusion body cell leading edge axolemma leading edge membrane neuron projection membrane plasma membrane region cell projection membrane neuronal cell body polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer microtubule cytoskeleton mitochondrion glial cell projection growth cone distal axon site of polarized growth

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth Z], H [auth P], I [auth X]	IPR027324	Microtubule associated protein MAP2/MAP4/Tau	Family
G [auth Z], H [auth P], I [auth X]	IPR001084	Microtubule associated protein, tubulin-binding repeat	Repeat
G [auth Z], H [auth P], I [auth X]	IPR002955	Microtubule-associated protein Tau	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
G [auth Z], H [auth P], I [auth X]	Pharos: P10636	Pick disease Alzheimer disease progressive supranuclear palsy frontotemporal dementia Parkinson disease dementia tauopathy neurodegenerative disease progressive supranuclear palsy-parkinsonism syndrome Memory Disorders semantic dementia idiopathic pulmonary fibrosis late-onset Parkinson disease atrial fibrillation respiratory failure Pick disease Alzheimer disease progressive supranuclear palsy frontotemporal dementia Parkinson disease dementia tauopathy neurodegenerative disease progressive supranuclear palsy-parkinsonism syndrome Memory Disorders semantic dementia idiopathic pulmonary fibrosis late-onset Parkinson disease atrial fibrillation respiratory failure supranuclear palsy, progressive, 1 behavioral variant of frontotemporal dementia bipolar disorder subependymal giant cell astrocytoma chronic obstructive pulmonary disease oligodendroglioma osteosarcoma parkinsonian disorder amyotrophic lateral sclerosis malignant ependymoma breast cancer osteoarthritis toxic encephalopathy ovarian cancer glioblastoma pilocytic astrocytoma intellectual disability androgenetic alopecia attention deficit hyperactivity disorder, inattentive type malignant glioma cardiomyopathy cutaneous lupus erythematosus osteoarthritis, hip endogenous depression hepatocellular carcinoma amyloidosis large cell medulloblastoma progressive non-fluent aphasia aphasia learning disability lung carcinoma psoriasis atypical teratoid rhabdoid tumor medulloblastoma autosomal recessive juvenile Parkinson disease 2

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
G [auth Z], H [auth P], I [auth X]	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.